diff qiime2-2020.8/qiime_emperor_biplot.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_emperor_biplot.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,117 @@
+<?xml version="1.0" ?>
+<tool id="qiime_emperor_biplot" name="qiime emperor biplot"
+      version="2020.8">
+  <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime emperor biplot
+
+--i-biplot=$ibiplot
+# if $input_files_msamplemetadatafile:
+  # def list_dict_to_string(list_dict):
+    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+    # for d in list_dict[1:]:
+      # set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
+# end if
+# if $input_files_mfeaturemetadatafile:
+  # def list_dict_to_string(list_dict):
+    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+    # for d in list_dict[1:]:
+      # set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
+# end if
+
+#if $pignoremissingsamples:
+ --p-ignore-missing-samples
+#end if
+
+#if $pinvert:
+ --p-invert
+#end if
+
+--p-number-of-features=$pnumberoffeatures
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odistancematrix.qza $odistancematrix
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties(\'biplot\') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data" />
+    <repeat name="input_files_msamplemetadatafile" optional="False" title="--m-sample-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple          The sample metadata arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA... (multiple          The feature metadata (useful to manipulate the arrows arguments will    in the plot). be merged)                                                     [optional]" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
+    <param label="--p-invert: --p-invert: / --p-no-invert If specified, the point and arrow coordinates will be swapped.                               [default: False]" name="pinvert" selected="False" type="boolean" />
+    <param label="--p-number-of-features: INTEGER Range(1, None)     The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).          [default: 5]" min="1" name="pnumberoffeatures" optional="True" type="integer" value="5" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Visualize and Interact with Principal Coordinates Analysis Biplot
+###############################################################
+
+Generates an interactive ordination biplot where the user can visually
+integrate sample and feature metadata. Vectors representing the n most
+important features are then plotted in the emperor visualization (5
+largest, by default).
+
+Parameters
+----------
+biplot : PCoAResults % Properties('biplot')
+    The principal coordinates matrix to be plotted.
+sample_metadata : Metadata
+    The sample metadata
+feature_metadata : Metadata, optional
+    The feature metadata (useful to manipulate the arrows in the plot).
+ignore_missing_samples : Bool, optional
+    This will suppress the error raised when the coordinates matrix
+    contains samples that are not present in the metadata. Samples without
+    metadata are included by setting all metadata values to: "This sample
+    has no metadata". This flag is only applied if at least one sample is
+    present in both the coordinates matrix and the metadata.
+invert : Bool, optional
+    If specified, the point and arrow coordinates will be swapped.
+number_of_features : Int % Range(1, None), optional
+    The number of most important features (arrows) to display in the
+    ordination. “Importance” is calculated for each feature based on the
+    vector’s magnitude (euclidean distance from origin).
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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